Mona Singh - Publications

Affiliations: 
Computer Science Princeton University, Princeton, NJ 
Area:
Computational molecular biology, as well as its interface with machine learning and algorithms.

64 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Munro D, Ghersi D, Singh M. Two critical positions in zinc finger domains are heavily mutated in three human cancer types. Plos Computational Biology. 14: e1006290. PMID 29953437 DOI: 10.1371/journal.pcbi.1006290  0.56
2017 Pritykin Y, Brito T, Schupbach T, Singh M, Pane A. Integrative analysis unveils new functions for the Drosophila Cutoff protein in non-coding RNA biogenesis and gene regulation. Rna (New York, N.Y.). PMID 28420675 DOI: 10.1261/rna.058594.116  1
2015 Wang NC, Singh M, Adelstein EC, Jain SK, Mendenhall GS, Shalaby AA, Voigt A, Saba S. New Onset Left Bundle Branch Block-Associated Idiopathic Nonischemic Cardiomyopathy and Left Ventricular Ejection Fraction Response to Guideline-Directed Therapies: The NEOLITH Study. Heart Rhythm : the Official Journal of the Heart Rhythm Society. PMID 26688064 DOI: 10.1016/j.hrthm.2015.12.020  0.36
2015 Ochoa A, Storey JD, Llinás M, Singh M. Beyond the E-Value: Stratified Statistics for Protein Domain Prediction. Plos Computational Biology. 11: e1004509. PMID 26575353 DOI: 10.1371/journal.pcbi.1004509  1
2015 Pritykin Y, Ghersi D, Singh M. Genome-Wide Detection and Analysis of Multifunctional Genes. Plos Computational Biology. 11: e1004467. PMID 26436655 DOI: 10.1371/journal.pcbi.1004467  1
2015 Nadimpalli S, Persikov AV, Singh M. Pervasive variation of transcription factor orthologs contributes to regulatory network evolution. Plos Genetics. 11: e1005011. PMID 25748510 DOI: 10.1371/journal.pgen.1005011  1
2015 Persikov AV, Wetzel JL, Rowland EF, Oakes BL, Xu DJ, Singh M, Noyes MB. A systematic survey of the Cys2His2 zinc finger DNA-binding landscape. Nucleic Acids Research. 43: 1965-84. PMID 25593323 DOI: 10.1093/nar/gku1395  1
2014 Ghersi D, Singh M. molBLOCKS: decomposing small molecule sets and uncovering enriched fragments. Bioinformatics (Oxford, England). 30: 2081-3. PMID 24681908 DOI: 10.1093/bioinformatics/btu173  1
2014 Jiang P, Singh M. CCAT: Combinatorial Code Analysis Tool for transcriptional regulation. Nucleic Acids Research. 42: 2833-47. PMID 24366875 DOI: 10.1093/nar/gkt1302  1
2014 Ghersi D, Singh M. Interaction-based discovery of functionally important genes in cancers. Nucleic Acids Research. 42: e18. PMID 24362839 DOI: 10.1093/nar/gkt1305  1
2014 Persikov AV, Rowland EF, Oakes BL, Singh M, Noyes MB. Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets. Nucleic Acids Research. 42: 1497-508. PMID 24214968 DOI: 10.1093/nar/gkt1034  1
2014 Persikov AV, Singh M. De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins. Nucleic Acids Research. 42: 97-108. PMID 24097433 DOI: 10.1093/nar/gkt890  1
2013 Pritykin Y, Singh M. Simple topological features reflect dynamics and modularity in protein interaction networks. Plos Computational Biology. 9: e1003243. PMID 24130468 DOI: 10.1371/journal.pcbi.1003243  1
2013 Jiang P, Singh M, Coller HA. Computational assessment of the cooperativity between RNA binding proteins and MicroRNAs in Transcript Decay. Plos Computational Biology. 9: e1003075. PMID 23737738 DOI: 10.1371/journal.pcbi.1003075  1
2013 Berger B, Peng J, Singh M. Computational solutions for omics data. Nature Reviews. Genetics. 14: 333-46. PMID 23594911 DOI: 10.1038/nrg3433  1
2013 Song J, Singh M. From hub proteins to hub modules: the relationship between essentiality and centrality in the yeast interactome at different scales of organization. Plos Computational Biology. 9: e1002910. PMID 23436988 DOI: 10.1371/journal.pcbi.1002910  1
2013 Ghersi D, Singh M. Disentangling function from topology to infer the network properties of disease genes. Bmc Systems Biology. 7: 5. PMID 23324116 DOI: 10.1186/1752-0509-7-5  1
2013 Kahveci T, Singh M. Guest editorial for ACM BCB Ieee/Acm Transactions On Computational Biology and Bioinformatics. 10: 1089-1090. DOI: 10.1109/TCBB.2013.182  1
2012 Khan Z, Bloom JS, Amini S, Singh M, Perlman DH, Caudy AA, Kruglyak L. Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS. Molecular Systems Biology. 8: 602. PMID 22893000 DOI: 10.1038/msb.2012.34  1
2011 Khan Z, Amini S, Bloom JS, Ruse C, Caudy AA, Kruglyak L, Singh M, Perlman DH, Tavazoie S. Accurate proteome-wide protein quantification from high-resolution 15N mass spectra. Genome Biology. 12: R122. PMID 22182234 DOI: 10.1186/gb-2011-12-12-r122  1
2011 Kingsford C, Zaslavsky E, Singh M. A cost-aggregating integer linear program for motif finding. Journal of Discrete Algorithms (Amsterdam, Netherlands). 9: 326-334. PMID 22081765 DOI: 10.1016/j.jda.2011.04.001  1
2011 Pane A, Jiang P, Zhao DY, Singh M, Schüpbach T. The Cutoff protein regulates piRNA cluster expression and piRNA production in the Drosophila germline. The Embo Journal. 30: 4601-15. PMID 21952049 DOI: 10.1038/emboj.2011.334  1
2011 Persikov AV, Singh M. An expanded binding model for Cys2His2 zinc finger protein-DNA interfaces. Physical Biology. 8: 035010. PMID 21572177 DOI: 10.1088/1478-3975/8/3/035010  1
2011 Ochoa A, Llinás M, Singh M. Using context to improve protein domain identification. Bmc Bioinformatics. 12: 90. PMID 21453511 DOI: 10.1186/1471-2105-12-90  1
2010 Capra JA, Pollard KS, Singh M. Novel genes exhibit distinct patterns of function acquisition and network integration Genome Biology. 11. PMID 21187012 DOI: 10.1186/gb-2010-11-12-r127  1
2010 Capra JA, Paeschke K, Singh M, Zakian VA. G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae. Plos Computational Biology. 6: e1000861. PMID 20676380 DOI: 10.1371/journal.pcbi.1000861  1
2010 Jiang P, Singh M. SPICi: a fast clustering algorithm for large biological networks. Bioinformatics (Oxford, England). 26: 1105-11. PMID 20185405 DOI: 10.1093/bioinformatics/btq078  1
2010 Przytycka TM, Singh M, Slonim DK. Toward the dynamic interactome: it's about time. Briefings in Bioinformatics. 11: 15-29. PMID 20061351 DOI: 10.1093/bib/bbp057  1
2010 Berger-Wolf TY, Przytycka TM, Singh M, Slonim DK. Dynamics of biological networks: Session introduction Pacific Symposium On Biocomputing 2010, Psb 2010. 120-122.  1
2010 Moulton V, Singh M. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6293.  1
2010 Berger-Wolf TY, Przytycka TM, Singh M, Slonim DK. Dynamics of biological networks: Session introduction Pacific Symposium On Biocomputing 2010, Psb 2010. 120-122.  1
2009 Capra JA, Laskowski RA, Thornton JM, Singh M, Funkhouser TA. Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure. Plos Computational Biology. 5: e1000585. PMID 19997483 DOI: 10.1371/journal.pcbi.1000585  1
2009 Song J, Singh M. How and when should interactome-derived clusters be used to predict functional modules and protein function? Bioinformatics (Oxford, England). 25: 3143-50. PMID 19770263 DOI: 10.1093/bioinformatics/btp551  1
2009 Khan Z, Bloom JS, Garcia BA, Singh M, Kruglyak L. Protein quantification across hundreds of experimental conditions. Proceedings of the National Academy of Sciences of the United States of America. 106: 15544-8. PMID 19717460 DOI: 10.1073/pnas.0904100106  1
2009 Bloom JS, Khan Z, Kruglyak L, Singh M, Caudy AA. Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays. Bmc Genomics. 10: 221. PMID 19435513 DOI: 10.1186/1471-2164-10-221  1
2009 Khan Z, Bloom JS, Kruglyak L, Singh M. A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays. Bioinformatics (Oxford, England). 25: 1609-16. PMID 19389736 DOI: 10.1093/bioinformatics/btp275  1
2009 Yanover C, Singh M, Zaslavsky E. M are better than one: an ensemble-based motif finder and its application to regulatory element prediction. Bioinformatics (Oxford, England). 25: 868-74. PMID 19223448 DOI: 10.1093/bioinformatics/btp090  1
2009 Persikov AV, Osada R, Singh M. Predicting DNA recognition by Cys2His2 zinc finger proteins. Bioinformatics (Oxford, England). 25: 22-9. PMID 19008249 DOI: 10.1093/bioinformatics/btn580  1
2009 Banks E, Nabieva E, Chazelle B, Peterson R, Singh M. Analyzing and interrogating biological networks (abstract) Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5462: 14-15. DOI: 10.1007/978-3-642-00727-9_2  1
2008 Banks E, Nabieva E, Chazelle B, Singh M. Organization of physical interactomes as uncovered by network schemas. Plos Computational Biology. 4: e1000203. PMID 18949022 DOI: 10.1371/journal.pcbi.1000203  1
2008 Banks E, Nabieva E, Peterson R, Singh M. NetGrep: fast network schema searches in interactomes. Genome Biology. 9: R138. PMID 18801179 DOI: 10.1186/gb-2008-9-9-r138  1
2008 Capra JA, Singh M. Characterization and prediction of residues determining protein functional specificity. Bioinformatics (Oxford, England). 24: 1473-80. PMID 18450811 DOI: 10.1093/bioinformatics/btn214  1
2008 Singh MP, Shaw RK, Knutton S, Pallen MJ, Crepin VF, Frankel G. Identification of amino acid residues within the N-terminal domain of EspA that play a role in EspA filament biogenesis and function. Journal of Bacteriology. 190: 2221-6. PMID 18178741 DOI: 10.1128/JB.01753-07  1
2008 Nabieva E, Singh M. Protein Function Prediction via Analysis of Interactomes Prediction of Protein Structures, Functions, and Interactions. 231-258. DOI: 10.1002/9780470741894.ch10  1
2007 Capra JA, Singh M. Predicting functionally important residues from sequence conservation. Bioinformatics (Oxford, England). 23: 1875-82. PMID 17519246 DOI: 10.1093/bioinformatics/btm270  1
2007 Gusfield D, Ludäscher B, Singh M. Associate editor appreciation and welcome Ieee/Acm Transactions On Computational Biology and Bioinformatics. 4: 321. DOI: 10.1109/TCBB.2007.70234  1
2006 Zaslavsky E, Singh M. A combinatorial optimization approach for diverse motif finding applications. Algorithms For Molecular Biology : Amb. 1: 13. PMID 16916460 DOI: 10.1186/1748-7188-1-13  1
2006 Kingsford C, Zaslavsky E, Singh M. A compact mathematical programming formulation for DNA motif finding Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4009: 233-245. DOI: 10.1007/11780441_22  1
2005 Nabieva E, Jim K, Agarwal A, Chazelle B, Singh M. Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps. Bioinformatics (Oxford, England). 21: i302-10. PMID 15961472 DOI: 10.1093/bioinformatics/bti1054  1
2005 Kingsford CL, Chazelle B, Singh M. Solving and analyzing side-chain positioning problems using linear and integer programming. Bioinformatics (Oxford, England). 21: 1028-36. PMID 15546935 DOI: 10.1093/bioinformatics/bti144  1
2004 Osada R, Zaslavsky E, Singh M. Comparative analysis of methods for representing and searching for transcription factor binding sites. Bioinformatics (Oxford, England). 20: 3516-25. PMID 15297295 DOI: 10.1093/bioinformatics/bth438  1
2004 Brooks DJ, Fresco JR, Singh M. A novel method for estimating ancestral amino acid composition and its application to proteins of the Last Universal Ancestor. Bioinformatics (Oxford, England). 20: 2251-7. PMID 15073018 DOI: 10.1093/bioinformatics/bth235  1
2004 Fong JH, Keating AE, Singh M. Predicting specificity in bZIP coiled-coil protein interactions. Genome Biology. 5: R11. PMID 14759261  1
2004 Jim K, Parmar K, Singh M, Tavazoie S. A cross-genomic approach for systematic mapping of phenotypic traits to genes. Genome Research. 14: 109-15. PMID 14707173 DOI: 10.1101/gr.1586704  1
2004 Chazelle B, Kingsford C, Singh M. A semidefinite programming approach to side chain positioning with new rounding strategies Informs Journal On Computing. 16: 380-392. DOI: 10.1287/ijoc.1040.0096  1
2003 Craig L, Taylor RK, Pique ME, Adair BD, Arvai AS, Singh M, Lloyd SJ, Shin DS, Getzoff ED, Yeager M, Forest KT, Tainer JA. Type IV pilin structure and assembly: X-ray and EM analyses of Vibrio cholerae toxin-coregulated pilus and Pseudomonas aeruginosa PAK pilin. Molecular Cell. 11: 1139-50. PMID 12769840 DOI: 10.1016/S1097-2765(03)00170-9  1
2003 Chazelle B, Kingsford C, Singh M. The Side-Chain Positioning Problem: A Semidefinite Programming Formulation with New Rounding Schemes Principles of Computing and Knowledge: Paris C. Kanellakis Memorial Workshop. 86-94.  1
2002 Brooks DJ, Fresco JR, Lesk AM, Singh M. Evolution of amino acid frequencies in proteins over deep time: inferred order of introduction of amino acids into the genetic code. Molecular Biology and Evolution. 19: 1645-55. PMID 12270892  1
2001 Malashkevich VN, Singh M, Kim PS. The trimer-of-hairpins motif in membrane fusion: Visna virus Proceedings of the National Academy of Sciences of the United States of America. 98: 8502-8506. PMID 11447278 DOI: 10.1073/pnas.151254798  1
2001 Singh M, Kim PS. Towards predicting coiled-coil protein interactions Proceedings of the Annual International Conference On Computational Molecular Biology, Recomb. 279-286.  1
2000 Zhao X, Singh M, Malashkevich VN, Kim PS. Structural characterization of the human respiratory syncytial virus fusion protein core Proceedings of the National Academy of Sciences of the United States of America. 97: 14172-14177. PMID 11106388 DOI: 10.1073/pnas.260499197  1
1999 Singh M, Berger B, Kim PS. LearnCoil-VMF: Computational evidence for coiled-coil-like motifs in many viral membrane-fusion proteins Journal of Molecular Biology. 290: 1031-1041. PMID 10438601 DOI: 10.1006/jmbi.1999.2796  1
1998 Singh M, Berger B, Kim PS, Berger JM, Cochran AG. Computational learning reveals coiled coil-like motifs in histidine kinase linker domains. Proceedings of the National Academy of Sciences of the United States of America. 95: 2738-43. PMID 9501159 DOI: 10.1073/pnas.95.6.2738  1
1997 Berger B, Singh M. Iterative method for improved protein structural motif recognition Proceedings of Thr Annual International Conference On Computational Molecular Biology, Recomb. 37-46.  1
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